Can the new Powerboost 1000 charger ID: 2465 deal with multiple voltage inputs like the Poly solar charger and be able to have the 3.7 4400mah battery plugged in with a Raspberry Pi on the load and then on voltage input, use 5v solar cells and or USB? so if the output was off the solar cells could charge the battery or if USB was plugged it it would charge the battery too. With the output on, it would run the Pi off the battery and if the solar cells are getting enough sun then charge the battery/ maintain battery voltage? The poly solar charger alone doesn't boost the output of the 3.7v batteries to 5v or maintain 5v output unless either getting 5v from USB or from solar right?

Component changes in that part of the circuit may affect efficiency. The datasheet for the boost control chip gives you recommended starting parameters. But you need to test it in-circuit.to see how it actually performs.